Knowing where to look for advice can be an important part of problem solving in bioinformatics.
The following websites & discussion boards are well populated with experienced people across a wide variety of topics in programming, mathematics & bioinformatics, and can be a very helpful first port of call when you're stuck.
The Research Data Storage Infrastructure (RDSI) Project is an initiative of the National Collaborative Research Infrastructure Strategy, is funded from the Education Investment Fund under the Super Science (Future Industries) initiative. Secure Data Storage is available upon request.
The Bioinformatics Hub has a GitHub account which contains much of our public analytic code. Hopefully this is an informative site for those who look through our work.
Most research performed by the Bioinformatics Hub utilises the Phoenix HPC cluster located within the University of Adelaide.
Visit the Phoenix High Performance Computing for more information, or to sign up for an account. Training workshops in the usage of this resource are also run regularly, so please check the Training & Workshops page for the next scheduled session
Some key bioinformatics tools & their sources are:
Packages in current development by the Bioinformatics Hub
- ngsReports : Easier R handling of multiple NGS reporting files, such as FASTQC output and log files from common alignment tools
- strandCheckR : Check strandedness of RNA Seq alignments. Also able to be used for removal of genomic DNA sequences for libraries with incomplete DNA removal
Tools for NGS Data
If you are unsure about the installation or use of any NGS tools, please email the Bioinformatics Hub to see if we can help.
Many NGS tools are now able to be installed using Git. An installation is available for all platforms is available.
- BAMTools - For easy handling of BAM files.
- BEDTools - a software package for manipulating BED files, with some utilities working with BAM. Built upon BAMTools.
- Cutadapt - for trimming adapter sequences from NGS reads
- GATK - the Genome Analysis Toolkit. Rich funtionality including an accurate SNP caller. Built upon Picard.
- SAMTools - various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format
- sambamba - Faster implementations of many SAMTools functions
- Picard - a suite of java-based tools for data exploration
- BWA - Burrows-Wheeler Aligner for short and long reads.
- Bowtie - Highly efficient short read aligner. Natively support SAM output in recent version.
- HISAT2 - The main RNA-Seq aligner used by the Boinformatics Hub
- TopHat - for mapping short RNA-seq reads bridging exon junctions.
- STAR - An RNA-Seq aligner implemented in parallel for additional speed
Other Helpful Tools
- FASTQC - A quality control tool for high throughput sequence data.
- Galaxy - is an online collection of NGS tools accessible via a Graphical User Interface (GUI) for those with minimal command-line experience